Reference SNP(refSNP) Cluster Report: rs6151408

Reference SNP(refSNP) Cluster Report: rs6151408

refSNP ID: rs6151408
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	114/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/G
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_000487.4:c.-142C>G
NM_001085425.1:c.-37C>G
NM_001085426.1:c.-20+31C>G
NM_001085427.1:c.-20+76C>G
NM_001085428.1:c.-35+31C>G
NT_011526.6:g.286406G>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss61715650 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6151408 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss8485009	EGP_SNPS\|ARSA-001209		fwd/T	C/G	gtactgtcgggccccggccctctggagctt	aggaggcggccgtcagggtcggggagtatt	04/18/03	04/07/04	114	Genomic			unknown
ss61715650	SI_EXO\|NT_011526.6_286406		rev/	C/G	aatactccccgaccctgacggccgcctcct	aagctccagagggccggggcccgacagtac	07/11/06	03/31/08	127	Genomic			unknown

Fasta sequence (Legend)

 CCCAGAGCCC GTTTCAAGAC CGCAGCCAAC AGCCTCAGGC GCACACGGCG GCCTCGGAGC
 GAGCACGCGC AGCAACGCCC CTCGCCCCGG CCCGCCCCCG GCCCCGCCCC CGGCCCCGCC
 CCCGGCCCCG CCCCGCAAGG GTCACAGGTC ACGGGGCGGG GCCGAGGCGG AAGCGCCCGC
 AGCCCGGTAC CGGCTCCTCC TGGGCTCCCT CTAGCGCCTT CCCCCCGGCC CGACTCCGCT
 GGTCAGCGCC AAGTGACTTA CGCCCCCGAC CCTGAGCCCG GACCGCTAGG CGAGGAGGAT
 CAGATCTCCG CTCGAGAATC TGAAGGTGCC CTGGTCCTGG AGGAGTTCCG TCCCAGCCCG
 CGGTCTCCCG GTACTGTCGG GCCCCGGCCC TCTGGAGCTT
 S
 AGGAGGCGGC CGTCAGGGTC GGGGAGTATT TGGGTCCGGG GTCTCAGGGA AGGGCGGCGC
 CTGGGTCTGC GGTATCGGAA AGAGCCTGCT GGAGCCAAGT AGCCCTCCCT CTCTTGGGAC
 AGACCCCTCG GTCCCATGTC CATGGGGGCA CCGCGGTCCC TCCTCCTGGC CCTGGCTGCT
 GGCCTGGCCG TTGCCCGTCC GCCCAACATC GTGCTGATCT TTGCCGACGA CCTCGGCTAT
 GGGGACCTGG GCTGCTATGG GCACCCCAGC TCTACCACTC CCAACCTGGA CCAGCTGGCG
 GCGGGAGGGC TGCGGTTCAC AGACTTCTAC GTGCCTGTGT CTCTGTGCAC ACCCTCTAGG
 TAAAGAGGGG GCCGCGCCTC TTCCCCGCCC CGACCCTCCA

GeneView

GeneView via analysis of contig annotation: ARSA arylsulfatase A

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_011526->NM_000487

function

reference

NT_011526->NM_001085425

function

reference

NT_011526->NM_001085426

function

reference

NT_011526->NM_001085427

function

reference

NT_011526->NM_001085428

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function


reference	NT_011526->NM_000487->	286406	reverse	265	5' UTR

reference	NT_011526->NM_001085425->	286406	reverse	265	5' UTR

reference	NT_011526->NM_001085426->NP_001078895	286406	reverse		intron

reference	NT_011526->NM_001085427->NP_001078896	286406	reverse		intron

reference	NT_011526->NM_001085428->NP_001078897	286406	reverse		intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs6151408 maps exactly once on NCBI human chromosome 22

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
22	NW_001838756.2	143638	33956745	plus	C	alt_assembly_8	HuRef	HuRef	view	400
22	NW_927650.1	8122002	34942369	minus	G	alt_assembly_1	Celera	Celera	view	400
22	NT_011526.6	286406	49413209	minus	G	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011526.6

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Draft:
NM_000487.4 NM_001085425.1	L49235.2

UniGene Cluster ID
88251

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss61715650	HapMap-CEU	European	120	IG			1.000			1.000

	HapMap-HCB	Asian	90	IG	1.000				1.000

	HapMap-JPT	Asian	88	IG	1.000				1.000

	HapMap-YRI	Sub-Saharan African	120	IG	1.000				1.000

ss8485009	PDR90	Global	174	IG	0.966	0.034		1.000	0.983	0.017

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.329+/-0.237	360	300	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	YES

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Revised: May 25, 2006 1:38 PM .